Hi Doug
I still use the old white T-Shirt method, I point the telescope at a clear blue sky as far away from the sun as possible, take some test exposure and check that the Historgram is offset to the left third of the frame and take about 20 or so RAW's. As you have already said, the colour dosen't matter when the Master Flat is made.
I have the camera in the same orientation and focus position as when my Lights are taken although there is another school of thought that advocates rotating the camera 90 degrees after each 5 or so exposures, not sure about that one though
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Cheers